Snippets

One of the ongoing projects and collaborations the ScienceVis Lab has been involved in relates to how animations of dynamic processes are mentally processed and how educational animations can be designed to facilitate this processing.For an upcoming educational study, we are designing stimuli that depict ant locomotion. For these stimuli, we require a realistic ant model and rig, which I have been working on recently. The rigging process involved determining what controls would be necessary, with the ability to match data from primary literature sources by verifying measurements of angles and distances on the model.This animated gif shows a few of the possible model motions in action.Detail and textures were sculpted on to the model to increase the perception of realism.The design of the dynamic nature of the stimuli is still in progress, but hopefully soon we will see this ant walking.

Through the molecular visualization work that we have been doing, a number of processes have been explored that may be worthwhile sharing with the broader science visualization community. Here are two tutorials that explore the use of Molecular Maya to help visualize macromolecules.

At the AMI annual conference in Atlanta Georgia, Stuart presented on Molecular Visualization and how we make decisions about representing molecular structure, motion, and interactions. Watch the online version of this presentation:

The workshop is titled “Visual Storytelling in Molecular Animation: Accuracy and Design” and covers the unique challenges of creating visual narratives in the molecular world. For one thing, you’d be too small to hold a pencil. Oh, I mean creating narratives about the molecular world.

We’ll cover molecular-scale phenomena and narrative design that takes these into account. There will be an exercise that puts the discussed ideas into practice. The exercise resource booklet can be downloaded here, along with a standalone storyboard template used in the workshop.

A new molecular visualization principle has been added to our project page. The “Show Protein Flexibility” principle conveys the idea that macromolecules like proteins have internal freedom of motion that allows for specific functionality. In this example, the membrane protein Cadherin has five extracellular domains linked by short flexible regions.

The “Best practices for visual storytelling in science” workshop was a great success, with 18 participants and three instructors (Gaël, Jodie, and Stuart). After discussing the challenges of visual storytelling at the molecular scale, design principles, cinematography, and storyboarding techniques, the participants embraced the task of creating storyboards to communicate a section of a signalling pathway.

Andrea and Stuart created resources to assist in the storyboarding exercise. A simple illustrated view of the pathway provided context and an overall understanding of the science. The participants used a supplied character sheet to assist with the sketching process.

We set up a custom projection system so that the individual groups of 3-4 people could share their work with everyone.

Small molecules typically use CPK space-filling or ball and stick representations, because surface meshes aren’t very informative. It’s more interesting to see structures like benzene rings when present. In order to bring the associated small molecule in with the protein structure I was importing using Molecular Maya, it was necessary to ensure that the HETATMs option was checked in the import options.

For the protein component, I kept the established simplified surface mesh used in the series so far. I decided on a modified ball and stick representation with pinched bonds, which Molecular Maya is capable of generating. The requirements of the animation and rendering process were such that I really needed regular geometry for the atoms and bonds, respectively balls and sticks. However, in the version of the software I was using, these structures were built with spherical particles and geometry instanced to particles. Maya unfortunately doesn’t have a particle instance to regular geometry conversion tool, so I was left to find my own workaround for this task. I’m confident that in the future, either or both of Autodesk Maya and Molecular Maya will have the capability of automatically performing the following, but at the time, this process was not implemented in the software.

First, I needed access to the underlying nodes in the mMaya hierarchy. I did this by selecting the mMaya node prefixed with pdbMolStruc_ and running the below code.

Note: this webpage has likely converted the regular quote marks to “smart quotes”, which will need to be replaced in your script editor with “straight quotes”.

Gaël McGill, Stuart Jantzen, & Jodie Jenkinson will be giving a workshop at the upcoming VizBi (Visualizing Biological Data) meeting in Heidelberg, Germany on March 8, 2016. The workshop is titled “Best practices for visual storytelling in science” and will be composed of three parts.

In the first section, an introduction to design principles for visual communication will be discussed, with specific examples tied to biological visualization. The second section will explore a number of visualization guidelines that relate to molecular behaviours and cellular environments. These guidelines are exemplified by the paired visualization examples that we have been developing. The final section will involve a group discussion and collaborative iteration on a storyboard treatment that we will provide. Combining the design principles and guidelines introduced in the first and second parts of the workshop, attendees will explore solutions to the storytelling challenges inherent in the accurate depiction of molecular scale phenomena.

Registration for the conference and workshops can be found through this link. We hope to see you there!

As part of one of the Molecular Visualization Principles, I am attempting to design a simulation of molecular water with correct scale, density, and an approximation of brownian motion.

I began by creating a very simple water molecule model, ensuring that the dimensions were accurate. Okay, the bond angles might be very slightly out, but who would ever be able to tell? I knew there were going to be a huge number of copies, so keeping the poly count low was a must.

When making the simulation, I decided to ignore hydrogen bonding interactions, but I did use the bonding radius for the collision radius, which created a natural looking separation between the molecules.

In order to determine how the simulation would look once rendered, I made a small cube’s worth of molecules at the size, speed, and resolution I would be using for the final animation. This is the reason it takes up only a small part of the frame. If the result was a fuzzy blurry mess, I would know that changes were required.

A used a hand animated sphere as a collider and included noisy turbulence to induce brownian motion. The final animation will include a lateral wipe to show and hide the water, so I made sure to include a simple test of that. The result is below, and I think it is successful enough to move on to the full scale simulation.